Looking back, several research and developmental organizations have contributed significantly to the reclamation and management of salt-affected lands.But they have been mostly working in isolation without interdisciplinary efforts.Considering the magnitude and complexity of the salinity problem, a holistic multidisciplinary and networking approach is required using a systems approach to tailor technologies across scales from the field to the district and the whole ecosystem.Moreover, key policy impediments must be addressed for rapid technology dissemination.These include effective involvement of stakeholders at the community level, provision of incentives such as subsidies and cost sharing, and enacting new laws that enforce reclamation requirements for maintenance and operation of SSD.Web-based platforms should be created to interface among policy planners, researchers, state agricultural departments and development boards, farmer’s associations, self-help groups and NGO’s.These will serve principally to ensure multi-stakeholder input when making decisions on the development and implementation of technologies, thereby accelerating the reclamation rate of saline-sodic soils.The State of Israel was established in 1948 and Israel’s recent history has been heavily influenced by the 1950 Law of Return,danish trolley granting Jewish people the right to immigrate to and settle in the country.Israel’s climate is arid to semi-arid, with two-thirds of its area being desert.

The average annual precipitation ranges from 25 mm in the Negev Desert, to about 300 mm in the coastal plains to 800 mm in the Upper Galilee region, occurring almost exclusively in the winter, between November and March.About two-thirds of the country’s fresh water supply has traditionally come from groundwater pumped from two major aquifers , with the other one-third coming from the Sea of Galilee, fed largely from the upper Jordan river.To ensure equitable distribution and efficient use of the available water resources, already in 1949 Israel enacted a legislative code that made water a public property that is under State control, with water licensing issued by its Water Commission.In order to supply water to Israel’s south, the National Water Carrier was built in the 1960s.About 50–55% of total consumed water is used for irrigation.However, to meet domestic and industrial freshwater demands, the fraction of natural freshwater used for irrigated agriculture has decreased from about two-thirds to currently about one-third.To supplement irrigation water needs, some 60%of the irrigation water supply now comes from treated wastewater and brackish groundwater.Finally, to ensure an adequate future water supply, Israel has embarked on building large-scale seawater desalination plants.In Israel, interest in soils and salts comes mostly from water scarcity and subsequent irrigation-induced salinity.The Israeli experience in salinity management of soils involves three unique intersecting aspects making the lessons learned of interest globally.The three aspects are:early and full adoption of highly efficient irrigation technologies including drip irrigation and knowledge driven scheduling,considerable amounts of relatively high salinity water from brackish groundwater and recycled municipal wastewater utilized for irrigation, and the recent large-scale move to desalination of seawater to insure national municipal water security that has led to reduction of salts in the water system, especially in recycled wastewater.

The lessons learned from Israel’s historical irrigation water policies and practices have been reviewed and discussed by Assouline et al., Tal , Siegel , and Raveh and Ben-Gal.Here we summarize in terms of salinity and soils.Israel is a small country with a relatively solid economic base, but isolated due to geo-political reality, and unique as a water-scarce country with successful agricultural development.Water consumption from all sources and for all sectors in Israel increased tenfold from 230 MCM in 1948 to 2200 MCM in 2018.It is estimated that only 55–65% of the present amount of the country’s water needs is renewed annually in its natural surface and groundwater resources.The remaining water supplied comes from groundwater mining, allocation of reclaimed wastewater, or by seawater desalination.While per capita consumption in the domestic and industrial sectors has remained essentially the same during these last decades, per capita water available for agricultural uses is less than half today than it was in the 1960s.Despite the reduction in water allocation, agricultural production per capita today is more than 150% of that produced 40 years ago.The success can be credited to several central driving principles including:intensification and modernization of agricultural systems;development and adoption of efficient water application technologies and methodologies; and establishment of reliable water sources for irrigation.Intensification and modernization of agriculture were accomplished in Israel by strong research and development programs, knowledge transfer to farmers by means of a solid extension service, and strong government economic support of national strategies.Drip irrigation was developed in Israel where this inherently efficient technology is used at rates higher than anywhere else in the world.Technologies and practices promoting water efficiency have further been encouraged by national water pricing and allocation strategies.

Utilization of low-quality water has been encouraged through a water for irrigation pricing structure where cost to farmers goes down as irrigation water salinity increases.The third principle stimulating success, a reliable source of water for irrigation, has been more difficult to accomplish.The NWC has historically conveyed water from the Sea of Galilee in the north to the south of Israel, seasonally mixing it on the way with various ground and floodwater sources.Average EC of the NWC water has historically ranged from 0.8 to 1.1 dS/m.Freshwater use in agriculture dropped from 950 MCM in 1998 to around 490 MCM today.Total water to agriculture has been maintained via the utilization of brackish and recycled water.Israel’s agriculture directly uses some 80 MCM of brackish groundwater with EC of more than 2 dS/m for irrigation, mainly in arid regions including along the Jordan Valley and the Arava and the Negev Highlands.Wastewater recycling has become a central component of Israel’s water management strategy.A master plan presented in 1956 envisioned the ultimate recycling of 150 MCM of sewage, all of which would go to agriculture.Today four times that level is recycled,vertical aeroponic tower garden representing around 85% of all domestic wastewater produced.Treated effluents today contribute roughly 25–30% of Israel’s total water supply and, depending on annual rainfall, up to 40% of the irrigation supply for agriculture.Salinity of recycled wastewater, depending on its type and origin, can range dramatically, but no matter what, salinity increases as the wastewater stream advances.In Israel, municipal recycled wastewater typically ranges from EC of1 to more than 3 dS/m.Israel’s agriculture directly uses some 80 MCM of brackish groundwater with EC of more than 2 dS/m for irrigation, mainly in arid regions including along the Jordan Valley and the Arava and the Negev Highlands.Wastewater recycling has become a central component of Israel’s water management strategy.A master plan presented in 1956 envisioned the ultimate recycling of 150 MCM of sewage, all of which would go to agriculture.Today four times that level is recycled, representing around 85% of all domestic wastewater produced.Treated effluents today contribute roughly 25–30% of Israel’s total water supply and, depending on annual rainfall, up to 40% of the irrigation supply for agriculture.Salinity of recycled wastewater, depending on its type and origin, can range dramatically, but no matter what, salinity increases as the wastewater stream advances.In Israel, municipal recycled wastewater typically ranges from EC of1 to more than 3 dS/m.Unfortunately, due to the high concentrations of salts in the irrigation water, Israel’s strategy for agricultural success seems to be not sustainable.Long-term application of salts to agricultural soils in a region where seasonal rainfall is low, unpredictable, and often insufficient to systematically mobilize and remove problematic salts, must include application of water designated to leach the accumulating salts out of the root zone.The water applied for leaching and leaving the root zone contains not only the salts that must be leached, but also various other contaminants, found naturally in the water, added in agricultural processes , or mobilized from soil and subsoil.

An example of problematic sustainability stemming from policy and practice of irrigation with water high in salts is found in the Arava desert where brackish groundwater is used to irrigate green and netho use protected vegetables.It is estimated that irrigation to leach salts in the region can be beneficial to yields and profits at rates as high as twice those necessary to satisfy crop evapotranspiration requirements.Regarding continued use of effluents or other salt-rich sources for irrigation water, additional indications of problems are found.These include the long-term increases in sodium adsorption ratio and exchangeable sodium percentage in soils , affecting soil structure and water infiltrability, a trend of increasing sodium and chloride found in irrigated plant tissues, and the tendency for Israeli fresh produce to have higher than international standards of sodium.In addition, there are increasing concerns regarding possible yet undiscovered detrimental long-term repercussions due to trace level contaminants in agricultural systems and the food chain.Despite all this, the latest responses of Israel to insure reliable municipal water supply to its growing population may coincidentally provide opportunity for a more sustainable solution for agriculture.Starting in 2007, Israel has added desalinated seawater to its water distribution stream.Desalination currently provides around 25% of Israel’s total water supply, as more than 40% of the country’s municipal water, often incidentally bringing very good quality water to agricultural areas and consistently reducing the salinity of recycled wastewater.Planned large-scale desalination in The Red Sea, as part of a project to stabilize Dead Sea water level by transporting the brine, would bring a significant amount of good quality water to replace current irrigation with brackish water to Israel.The Red-Dead conduit project, if funded and built, would additionally promote regional strategies for treating water scarcity and salinity together with Jordan and the Palestinian Authority.The turn to desalination as a strategy for water security is a positive opportunity to reverse the maybe dangerous and apparently non-sustainable trends consequential to irrigation with water containing high concentrations of salts.Treatment of brackish groundwater and of water specifically destined for irrigation may in the future benefit from technologies that, contrary to the current popular reverse osmosis based desalination, will selectively remove problematic monovalent ions while leaving agricultural desirable bivalent ions like calcium and magnesium.Israel is projecting that by 2050, two-third of its water supplies will come from treated effluent, desalinized or brackish water.Sustainable, healthy, economical, irrigated agriculture in Israel and other semi-arid and arid regions should be possible if the salts are taken out before application, instead of being allowed to negatively affect soils, crops, produce, and the environment.Latin America is a cultural entity extending from the Rio Grande in North America, to Tierra del Fuego, at the southernmost tip of South America.It is a vast area, spanning for 19.2 million km2 and home for approximately 650 million inhabitants, including countries with diverse availability of natural resources and economies.The Latin languages Spanish and Portuguese are the main tongues in the region, although English, French and Dutch are also spoken.This extensive territory features a huge variety of climates and soils, which lead to a great variability of ecosystems, and support an array of agricultural, livestock and forestry activities.Tropical to temperate/ cold crops are cultivated in it.Globally, the region is a net food exporter of a variety of primary products like grains , coffee, vegetables, and fruits, etc., and industrialized derivatives as sugar, vegetable oil, and wine.Unfortunately, estimations of the extension and distribution of salt-affected soils in Latin America are neither updated nor very precise, and partially based on expert judgment.Soil salinity and alkalinity are found in diverse environments throughout the region and include both primary and secondary salinity.Some estimations indicate that an area of about 7 105 km2 is affected by salinity and 6 105 km2 by sodicity, for a total salinized area of 1.3 suggest a total area of 1.7 106 km2 , however, other area estimations 106 km2.The total irrigated area is around 25–30 Mha.It is estimated that 25–50% of that area is affected by human-induced secondary salinization and sodification, adding approximately 4–5 Mha of recent human-induced salinization processes in non-irrigated areas.Primary salinization processes occur in the humid and sub-humid regions where natural saline, but mainly sodic soils are found.They are found in large plains with shallow saline or sodic ground-waters like the Chaco-Pampas regions, which are among the flattest sedimentary plains of the planet and a major grain exporter of the continent.

The new breeding lines are then tested in different soil types in different climatic zones within the regions of release, to ensure no yield penalty of the salt-tolerance gene.This approach of crossing and selection is usually done using molecular markers: DNA fragments that are associated with the trait.Selection for the trait itself is more laborious and expensive.Conventional breeding—For centuries, farmers in countries with extensive soil salinity have long been selecting best yielding crops for their land, as have the more recent commercial breeding companies.If their soil contains salt, they have selected salt-tolerant material without specifically intending to do so.An example is the salt-tolerant bread wheat Kharchia, which forms the basis of most of the salt-tolerant bread wheat germplasm released in India and Pakistan.Kharchia 65 is a land race developed from selections in farmers’ fields in the sodic-saline soils of the Kharchi-Pali area of Rajasthan.We do not yet know the physiological or molecular basis of the salt tolerance of Kharchia.For bread wheat a summary by Naeem et al.listed 14 varieties or land races under commercial production in India, Pakistan, Egypt and China.All of these were produced by conventional breeding.For rice, derivatives of the land races Pokkali or Nona Bokra which occur in the coastal regions of southern India have formed the basis of salt-tolerant rice cultivars.Ismail and Horielist 27 cultivars that have been released for salt tolerance between 2007 and 2014 for Bangladesh, the Philippines and India.These have been developed by conventional selection and breeding.The two most significant cultivars are CSR 36 for salt-affected soils in India, and BRRI Dhan 10 for soils inundated by seawater in coastal Bangladesh.We know the molecular basis of some of this salt tolerance: the presence of specific alleles of the Na+ transporter OsHKT1;5 that enhance Na+ exclusion.

These were identified in Nona Bokra as the QTL SKC1 and identified in Pokkali as the genomic region Saltol which encompasses OsHKT1;5.Molecular markers are now being used to accelerate breeding and to pyramid salt tolerance with other traits relevant to saline soils such as water logging tolerance.Trait-based breeding—A lack of fast and reliable screening methods has been the major limitation to exploring large germplasm collections,round plastic pots selecting genotypes with greater salt tolerance than the current cultivars, and introducing the salt tolerance into breeders’ advanced breeding lines for release of a new salt-tolerant cultivar.Munns and James summarized the various methods used in the laboratory or glasshouse to select for salt tolerance, along with their advantages and disadvantages.The simplest method is that of screening at germination as it is such a quick and easy test for large numbers of genotypes.However, for most species there is little or no correlation between genotypic differences in germination and genotypic differences in later growth or yield.The most reliable and useful method has been to measure rates of Na+ or Cl
accumulation in leaves, selecting individuals with low rates of accumulation.Ideally, biomass or grain yield should be the ultimate criterion for salt tolerance.Selections of various genotypes of pasture species like clover or alfalfa can conveniently be done in hydroponics or sand cultures with added salt, as cuts can be made every 6–8 weeks for replications.Cereals are more difficult to assess as grain yield needs to be measured in saline soil in the field, as does the yield of perennial horticultural species like citrus and grapevine.However, field experiments are plagued by heterogeneities in soil texture and surface elevation and its associated effect on soil salinity and compaction over short distances by influencing soil water deficits or water logging.This heterogeneity makes validation of breeding trials difficult as soil salinity varies greatly over area and depth.Soil salinity under each of a thousand or so breeding plots needs to be measured by electromagnetic induction with a simple-to-use meter such as Geonics EM38 after calibration.Incorporation of plot EC as a co-variant in the statistical analysis was essential to finding durum wheat genotypes and bread wheat and barley genotypes with higher yield in saline soil.

Over the last 20 years, selection of new salt-tolerant germplasm and its use in subsequent breeding has depended on traits and molecular markers for traits, which can be obtained from genetic analysis as Quantitative Trait Loci or by Genome Wide Association Studies.For many crop species, genetic variation in ion exclusion correlates highly with salt tolerance, and screening based on the measurement of ion accumulation in leaves is the most precise and effective form of selection, being quantitative and non-destructive.Examples include Na+ exclusion from leaves of durum wheat and rice.As an example, we describe a successful project on introduction of genes for salt tolerance from a wheat relative into a durum wheat cultivar, using molecular markers for the trait of Na+ exclusion.Durum wheat lacks the gene for Na+ exclusion found in bread wheat.Using the screening method of Na+ exclusion from leaves among 60 durum wheat relatives, Na+ exclusion equal to bread wheat was found in an unusual durum genotype named Line 149.Line 149 was crossed with the durum cultivar Tamaroi which had five times the leaf Na+ concentration and subsequent genetic analysis showed that Na+ exclusion was due to two genes that were named Nax1 and Nax2.Further crossing enabled separation of the two genes, which were identified as HKT1 transporters.Field trials in multiple sites showed that Nax2 increased yield on highly saline soil by 25% without affecting yield on better soils.However, Nax1 had a yield penalty that outweighed its advantage as a Na+ excluder.This yield penalty had not been obvious in glasshouse trials but became significant in the field.Phenomics—For crop species where a trait is multi-genic and covering different chromosome regions, molecular markers have limited value and selection is driven by phenomics.High-throughput phenotyping methods, now employed in the field as well as in the laboratory, allow large numbers of plants to be screened efficiently with limited handling and labor.Screening for salt tolerance in species which do not have a selectable salt-specific trait is only feasible using non-destructive methods.Such methods include biomass growth as assessed by photosynthesis, stomatal conductance, chlorophyll fluorescence and spectral reflectance.

Using color imaging along with nondestructive measurements of the leaf area and growth rate of each plant, it is possible to separate the effects of salinity on new leaf production from the acceleration of senescence and death of old leaves.Imaging allows the short-term osmotic effects on plant growth to be distinguished from the longer-term ionic effects.Infrared thermography is a widely used phenomic tool to detect differences between genotypes in soilless culture, pots, and field plots.In addition, hyperspectral imaging is used to quantify differences in water status and photosynthetic capacity and to detect genotypic differences in salinity tolerance, for example,hydroponic bucket among wheat cultivars after anthesis.Most candidate genes so far discovered and proven to be part of the mechanism of salt tolerance are membrane transporters for Na+, K+ or Cl.Few transcription factors have a known function, either in the downstream target genes, or the cells or tissues in which they operate.Genes involved in signaling pathways are not known to be specific for salinity but have commonalities with other abiotic stresses that reduce growth rate like drought, heat and cold.Transgenics—Use of the Arabidopsis genome has greatly accelerated the sequencing and functional analysis of candidate genes.In total there have been about 7300 papers on salt tolerance involving Arabidopsis.For the six main crop plants there are 9200.How much of this work has led to improving salt tolerance of crops in the field? A summary of 27 genes that have been over expressed in various crop species with “reported plant transgenic performance during salt stress” is listed by Roy et al.in their table 1, but with three exceptions, these transgenics have not been tested in the field or handed over to commercial plant breeders.In a review of genetic engineering for salinity tolerance in wheat , a list of 45 publications on wheat transformed with genes from other species, or other species transformed with genes from wheat, showed only one that included performance in the field; over expression of AtNHX1 improved grain yield of bread wheat.A notable success story is with barley: over expression of AVP1 increased biomass and yield in both non-saline and saline soil.Over expression of genes for accumulation of organic molecules that act as osmolytes such as proline have been studied for decades, but no cultivar has been released with enhanced proline accumulation that improves yield on saline soils.To date, QTL continues to be the main tool of genetic analysis for breeders, yet very few pre-breeding efforts have led to production of salt-tolerant cultivars.Similarly, the early optimism for GWAS to discover new loci for salinity tolerance and their subsequent utilization in varietal development is still not realized.

Success in has been hampered by lack of quantitative and repeatable measurements of the value of the trait to plant growth and yield in saline soil and selection of the best parents for QTL analysis or genotype array.Further research into selection techniques and germplasm diversity is needed.Key genes for Na+ transporters presented in Section 10.2 should be studied using species other than Arabidopsis.Crop species that are amenable to transformation and do not have complex genomes should be used.Omics methodologies should use relevant treatments, such as a gradual and moderate salt stress, not a severe and sudden one.Osmotic shocks cause plasmolysis and induce the synthesis of enzymes that repair the trauma caused to cells by their sudden shrinkage which may take at least 24 h to repair.Gene expression patterns are very different when the stress is imposed gradually compared to a salt shock.Cell-specific and tissue-specific expression is critical for the function of transporters and transcription factors, so studies should consider this should, for example, separately analyze growing from mature tissues.As take-up of genes for salt tolerance by commercial crop breeders has been so slow, and few studies arising with model plants such as Arabidopsis have been validated in the field, there is a high priority to engage plant breeders at an early stage of the project, working along with physiologists, molecular biologists and agronomists.Only then will molecular biology translate to the field and reach crop production targets.There are clear opportunities to make substantial yield gains by targeting basic strategic research, especially by utilizing pre-breeding results of undomesticated varieties, to improve abiotic stress tolerance of crops.Additional recommendations for future research include to use pre-breeding approaches seeking salt tolerance traits, rather than focus on model plants such as Arabidopsis.Also, while research at the cell level is likely to advance our physiological understanding of salt tolerance mechanisms, in parallel significant investments should be made at the field-level, employing the latest in phenotyping methodology.Summary: Unexplored and under-utilized biodiversity exists within crop species and their close relatives, which could be used to improve germplasm for crop production on salt-affected land, without resorting to GM methods that are at present unaccepted in many countries.Ongoing advances in rapid generation turnover, improved phenotyping, envirotyping and analytical methods can increase the rate of genetic gain in breeding.Further understanding of mechanisms at the molecular and physiological level will complement these new technologies and provide farmers with alternatives to increasing crop production on saline land.While genetic improvements cannot provide a permanent solution to increasing soil salinity, and salt-tolerant crops cannot de-salinize the land, a 10% increase in yield may double the famer’s profits, where the profit margin is small.In most of the salt-affected regions with dominance of sodium salts, salinity and sodicity are related, but they are different in terms of their effects on soil environments.“Salinity,” usually measured as total soluble salt concentration, affects plant growth and productivity through osmotic effects and ion toxicity or deficient effects on plant physiological processes.“Sodicity,” generally defined by soil ESPor SARof soil solution, causes constraints to plant growth through its effects on soil physical properties.Natural climatic and soil processes can lead to the formation of sodic soils from saline soils.In irrigated agriculture, the use of sodium containing waters leads to sodic soils by the adsorption of sodium by soils.Sodic soils with low salt concentration undergo structural degradation when wet because of swelling and clay dispersion, causing reduced water and air transport in near-surface soils and to limitations in soil aeration and infiltration.The effects of sodicity on soil physical properties are modified by soil salinity levels.

The soil salinity map derived from this updated Soils database is presented in Fig.5and is available on the FAO website.This updated information was largely needed to plan for land use changes that came about because of rising urban cities and growing rural populations, and to curb associated land degradation by erosion, pollution, salinity, as well as biodiversity losses.More recently, FAO through the Intergovernmental Technical Panel on Soils published the Status of the World’s Soil Resources report , intended to serve as a reference document on the status of global soil resources to support studies of regional assessment of soil change.It also contains a synthesis report for policy makers that summarizes its findings, conclusions, and recommendations.The SWSR report identifies the likely rapid increase of salt-affected soils globally and estimates that currently each year some 0.3–1.5Mha of farmland is taken out of production because of soil salinity problems.The SWSR report also states that about half of the total currently salt-affected soils are further decreasing their production potential.Annual economic costs were estimated to be about US $440 per ha of salt-induced agricultural land.Currently available maps continue to be out-of-date and too coarse for predicting trends on soil salinization.Global estimates of salinization combine different regional estimates that are not necessarily compatible.It is already noted that percentages vary widely between various literature sources.Across the world,fodder growing system countries and regions typically apply different soil classification systems, and as a result the definition of saline or sodic soils varies, thus changing the acreage of salt-affected lands.

A harmonized soil salinity classification system is needed that is universally applied.Gathering accurate, up-to-date information is critical for developing policies to halt the trend of increasing soil salinity across the world and regionally.Efforts to develop an updated and harmonized global soil salinity map were recently initiated by FAO through the Global Soil Partnership or GSP , through mapping of soil EC, SAR, and pH using existing country-level data.Soil salinity and the increase in areal extent is a serious global threat to agricultural production as soil degradation jeopardizes reaching a food-secure world.The only database that currently provides soil salinity data with global coverage is the Harmonized World Soil Database, but it is outdated and has several limitations when assessing changes in soil salinity and its areal extent.Except for a few country-focused reports, there is limited information on the world’s changing extent of salinized soils.Therefore, we recommend taking steps toward a new assessment.There are various reasons to suggest that the areal extent of soil salinization is increasing as well as becoming more severe.Information on such trends is extremely relevant as global and national policies on land use are being developed to advance Sustainable Development Goalsand to mitigate and/or adapt to climate change.Moreover, areas of salt-affected irrigated lands are inconclusive and vary between 25% and 50%depending on the data source.Soil salinization may be accelerating for several reasons including the changing climate.Rising temperatures increase soil evaporation and crop water requirements, enhancing soil salinization in areas already prone for salinity.Especially, coastal regions will be subjected to increasing risk of salinization by rising seawater levels, thereby pushing more saltwater into coastal aquifers, and increasing groundwater salinity.In addition, the likelihood of extreme storms and tsunamis can cause flooding of seawater, resulting in saltwater infiltration into soils and contaminating groundwater resources.

In his analysis of climate change impacts on soil salinization processes, Corwin states that the consequences of climate change have been overlooked and that changes in soil salinity extent will need to be monitored and mapped.He suggests that both proximal and remote sensors are the best methods to achieve this in a timely manner.Another reason that the area of saline soils is expanding relates to the increased use of marginal waters for irrigation, as decreased freshwater availability encourages application of treated wastewater or low salinity water for irrigation.Also, changing land uses from prime agricultural land to residential development promotes cultivation of more marginal lands, thereby enhancing the potential for land degradation.Furthermore, the decreasing availability of freshwater promotes more efficient irrigation methods such as drip and sprinkler irrigation, leading to reduced leaching of accumulated soil salts in regions with limited winter rains.Yet, to meet the world’s demand for nutritious food with the rising population, one may expect a further increase in irrigated area, especially in regions where freshwater availability is adequate.Lastly, salts accumulate over extended periods of continuous irrigation, thus further causing more salinity-prone areas over time.A universal global soil salinity map can be achieved using satellite imagery, soil properties maps, other land surface information, and advanced data analysis methods such as machine learning techniques.A recent example of such an approach was taken by Ivushkin et al., supported by the International Soil Reference and Information Centre.In their work, a total of six soil salinity maps were produced for 1986, 2000, 2002, 2005, 2009, 2016, using thermal IR imagery data from Landsat satellites.Their analysis presented a clear trend over this 20-year period, indicating that the global area of salt-affected soils increased from about 900 to 1000Mha, at an annual rate of about 2–5Mha/year.Various limitations of their methodology were given, including the need for higher spatial resolution, more ground truth data for regions with sparse data, uncertainty associated with temperature response due to plant variations in salt tolerance, and potential improvement using machine learning techniques.Salt-affected soils have significant impacts on the environment, freshwater availability, and agricultural production.Updated maps are needed to quantify soil salinization rates and to inform country level and new international policies and strategies to protect soils from further salinization.We urge prioritizing development of remote sensing instruments for future satellite missions that focus on observing spatial and temporal changes in land degradation, including soil erosion and salinity, at a global scale.

Detecting and monitoring soil salinity across agricultural regions is needed for inventorying soil resources; for identifying trends and drivers in salinization; and for judging the effectiveness of reclamation and conservation programs.Due to the impracticality of directly measuring root zone ECex over large areas , most regional-scale salinity assessment research has focused on alternative measures of salinity obtained through aerial photography and satellite remote sensing.Despite being developed many decades ago, remote detection of salinity has not been widely used in salinity monitoring programs and has achieved only limited success to date.However, methodological and technological advances made over the last 20 years suggest the routine use of remote sensing for monitoring agricultural salinity may be possible.Two approaches to remote salinity detection have been used: indirect and direct.With indirect methods, the level of root zone salinity is inferred based on crop growth and health,chicken fodder system usually as indicated by canopy spectral reflectance or thermographic data.The reflectance of certain visible or infrared spectra generally differs for healthy and stressed leaves.Thus, if a correlation between root zone ECex and spectral response can be established, regression or classifier models can be developed to quantify or label soil salinity levels in a remote sensing image.Direct methods detect salinity in bare soils based on the reflectance properties of surface salts and crusts.Sections of landscapes with and without surface salts can be distinguished due to the high reflectance of salt covered areas in the visible part of the spectrum.Within salt covered areas, salinity levels and salt types may be differentiated because of the effects that salt abundance, mineralogy, moisture, color, and surface crusting and roughness all have on reflectance.The direct approach is useful for assessing salt marshes and other highly saline, non-agricultural landscapes, as well as for tracking encroachment or appearance of barren, high salinity areas in dryland pastures and range lands.However, it has less utility for agricultural regions because of the presence of extensive vegetation.Therefore, we focus on indirect RS methods for soil salinity monitoring.By the middle of the 20th century, aerial photography and image analysis were touted as a means of inventorying crops and detecting disease.Portable or airborne spectral reflectance instruments did not exist, but laboratory measurements made on tissues from leaves in varying states of distress could reveal, for a given crop and development stage, the portion of the spectrum most sensitive to variations in leaf health.Aerial photographs sensitive to the identified spectral range could then be made using an appropriate combination of film and lens filter.

Through analysis of the aerial images, it was proposed that areas with healthy and diseased plants could be distinguished.Myers et al.were the first to connect aerial images of crops with root zone salinity.Working in Texas cotton fields, Myers et al.found that the salinity level in the 0.3–1.2m soil layer could be correlated with the spectral reflectance of cotton leaves, determined from aerial photographs using infrared film and a dark red filter that was sensitive at 675–900μm wavelengths.In a subsequent paper, Myers et al.reported it was possible to distinguish five levels of salinity and to estimate with reasonable accuracy the degree of salinity in the soil profile.It was also found that soil salinity could be predicted with reasonable accuracy from leaf temperatures measured with an infrared radiometer.Thomas et al.examined in greater detail the spectral reflectance of salt-affected cotton leaves and found that they changed during the growing season.At most wavelengths, percent reflectance from individual leaves was negatively correlated with salinity early in the year and positively correlated later.Multiple regression analyses of aerial image density indicated that under field conditions reflectance was influenced by soil salinity and percentage ground cover.The Landsat program and launch of the first operational Landsat satellite in 1972 spurred interest in using multi-spectral satellite imagery for natural resource management.Notable early examples of using space borne aircraft to detect salinity include identifying salt flats in Imperial Valley, California from photo images taken aboard Apollo 9and distinguishing saline from non-saline rangelands in South Texas using Skylab satellite imagery.The review of Metternicht and Zinck covers advances made during this period with respect to direct observation of visible surface salts.With the growing availability of multi-spectral reflectance data from satellites and other platforms, it became common from the 1970s onward to quantify multi-band canopy reflectance using vegetation indices such as the Normalized Difference Vegetation Index, NDVI¼/ , where R and NIR are spectral reflectance in the visible red and near-infrared bands, respectively.Wiegand et al.used imaging data from the SPOT-I satellite to evaluate the relationship of NDVI and the Greenness Vegetation Index to plant growth and yield in a single salt-affected, irrigated cotton field in Texas.Later, Wiegand et al.determined NDVI and GVI for four cotton fields in San Joaquin Valley , California using airborne photographic imagery made with multiple lens filters.Regression equations with NDVI and GVI as predictor variables were used to estimate salinity at about 100,000 pixels per field.The last 2 decades have seen a steady increase in the availability of remote sensing data, in the capabilities of various sensors and platforms, and in remote sensing applications.Even with improved technologies, a major problem with indirect salinity detection methods is that a single image generally cannot differentiate salinity-induced crop stress from stress caused by other factors such as weather, pests, and water management.Lobell et al.addressed this difficulty by evaluating multi-year data, hypothesizing that soil salinity is relatively constant compared to other more transient stressors.Lobell et al.found that using 6 years of reflectance data greatly improved the correlation between salinity and wheat yield, whereas Lobell et al.successfully evaluated regional-scale salinity using a 7-year average enhanced vegetation index derived from satellite MODIS data.Multi-temporal data was also used by Caccettaand Furby et al.for improved soil salinity classifications.Along the same lines, Zhang et al.used interpolated and integrated vegetation index time-series data as an explanatory variable rather than analyzing single-date data.Whitney et al.later applied the same integrated index method to the SJV and concluded that multi-year data further enhanced correlations with soil salinity.The use of environmental covariates as additional predictor variables in regression equations and classifiers has also improved accuracy.Scudiero et al.developed a linear regression equation for estimating soil salinity using spatial precipitation and temperature data, croptype data, and multi-temporal Landsat 7 ETM+ canopy reflectance data.They calibrated their model using data for thousands of Landsat 7 pixels at 30m resolution across 22 fields for which ground truth salinity data were available.For each 30 30m Landsat pixel, average root zone ECe for a 6-year period was modeled using the Canopy Response Salinity Index, CRSI, which combines spectral reflectance in the green, blue, red, and near-infrared bands.

The effect of flow on small-scale interactions between a benthic predator and zooplankton prey are more easily observed in a laboratory flume, where high-speed cameras can capture predator-prey events and prey type and concentration can be controlled. Knowing the flow environment in which these animals live can be used to recreate realistic flow conditions in a flume by matching the characteristics of flow observed over the organisms. Predators seek food under environmental conditions that can alter the outcome of predator-prey interactions. In the ocean, the motion of water varies due to tides, currents, waves, and turbulent eddies. How does this ambient flow impact feeding by marine organisms? Bottom-dwelling , predators that feed on small animals in the water column are dominant components of many marine communities. They play a key role in transporting material from pelagic systems in the water column down to the ocean floor .Visual predators such as burrow-dwelling fish dart out and catch passing plankton, while passive suspension feeders collect food delivered by ambient currents onto capture-surfaces. This study explores the effects of the flow of ambient water on these two contrasting modes of foraging. Passive suspension feeders rely on the motion of the surrounding water to transport prey to capture-surfaces, while active suspension feeders generate currents or actively pass a capture-surface through the water. Variations in the strength of the current can affect the amount of prey delivered to benthic suspension feeders and the ability of those predators to hold onto captured food. In response to flow, active suspension feeders can modify their feeding behavior,nft channel and passive suspension feeders can passively or actively alter their shape or orientation or grow into different configurations .

In shallow coastal habitats rapidly-changing currents, waves, and turbulence can impact feeding by benthic organisms. Currents reach maximumvelocities shoreward then seaward during flooding and ebbing tides, respectively, and minimum velocities at slack high and slack low tides. As waves approach the shore, the orbital motion of the water in the waves is compressed close to the substratum and oscillates back-and-forth on a scale of seconds . Turbulent eddies of different sizes stir the water. Many benthic zooplanktivores live in shallow coastal habitats where they are exposed to the turbulent reversals of flow associated with waves. Feeding rates by passive suspension feeders in unidirectional flow have been studied both theoretically and experimentally, e.g. in soft corals , bryozoans , sea pens , and sea anemones , but only a few experimental studies have explored the effects of waves and turbulence on rates of suspension feeding . The flow of water around benthic zooplanktivores can affect predator-prey interactions at each successive stage of the feeding process: encounter, capture, retention, and ingestion . The rate of encounters with prey is the number of prey that pass through the capture zone of a predator per time. As water velocity increases, more prey are swept past a benthic predator per time. In contrast, oscillating flow due to waves may lead to a predator resampling the same parcel of water, which could become depleted of prey. However, turbulent eddies of different sizes can stir the water and counteract depletion. Rothschild and Osborn modeled the role of turbulence in increasing encounter rates between predators and prey by such mixing, but their focus was on pelagic, not benthic, predators. Although it is informative to know how much food is available to a predator, rate of occurrences of encounters do not necessarily predict feeding rates that depend on the proportion of encountered prey that are captured , retained , and ingested.As prey pass by a predator, the escape behavior of motile planktonic prey that sense a nearby predator can reduce capture rates . Waves and turbulence can mask mechanical signals of the predator in the water and can disperse and dilute chemical signals, thereby inhibiting the ability of prey to detect and avoid the predator .

Retention is the ability of a predator to hold onto captured prey. Retention of a captured particle or organism depends on the stickiness of the predator, the contact area between the predator and prey, the size and shape of the captured item, and the speed of the water, as well as the ability of the captured prey to struggle and dislodge itself. It has been suggested and demonstrated in experiments conducted in unidirectional flow that reduced feeding rates by suspension feeders in rapidly-moving water are caused by drag forces that wash prey off capture-surfaces, but retention of prey in waves has not been analyzed. Ingestion can only occur if a predator is able to successfully retain prey. To understand the mechanisms underlying how turbulence affects the feeding rates of benthic predators that eat zooplankton, we must determine how the flow affects encounter rates , capture rates , and retention rates . If feeding rates scale with flow , rates of encounter, capture, and retention would increase proportionally. Previous studies of benthic zooplanktivorous fish showed that foraging behavior was affected by waves and turbulence . Tube blennies are small tropical fish that live in burrows within coral heads and actively dart out into the water column to capture passing zooplankton such as calanoid copepods. These suction-feeding fishes use vision to identify potential zooplanktonic prey, and then lunge towards the prey in a “predator approach”. The approach is successful when the fish swallows the prey, or unsuccessful when it misses the prey or the prey escapes and swims away. When exposed to increasing turbulence, the blennies reduced foraging effort . When exposed to waves, the blennies only tried to catch prey during the periods of slow flow that occurred as the water in the waves changed direction. However, foraging efficiency improved with increasing turbulence and stronger waves because the ability of evasive prey to detect and avoid predation declined with turbulent and wavy conditions . Although the blennies foraged less frequently, the fish were more successful at capturing prey. For these active zooplanktivores an increase in turbulence and waves interfered both with the predator’s feeding behavior and prey’s escape behavior,hydroponic nft but the net result was an increase in foraging success by the predator.

For passive suspension feeders dependent on flowing water to deliver prey, do increases in turbulence and stronger waves similarly impact capture rates and feeding efficiency? The effects of unidirectional flow on feeding rates of passive suspension-feeders are well studied . By quantifying feeding rates, only the retention or ingestion stage of the feeding process is observed, while the impacts of flow on encounter and capture of prey are obscured. Research examining the mechanisms used in passive suspension-feeding to encounter, capture, retain, and ingest prey has been carried out on non-motile “prey” and suggests that higher velocities of flow lead to higher rates of encounters and captures . Experiments with corals feeding on motile planktonic prey demonstrated that evasive swimming behavior by prey reduced capture rates in low flow and in waves . The research reported here examined how levels of turbulence and speed of waves affected each stage of the feeding process used by benthic suspension feeders eating zooplankton. The objective of this study was to measure how the trapping of motile zooplanktonic prey by passive benthic suspension feeders is affected by the “strength” of ambient flow across the predators. We addressed this question using sea anemones, Anthopleura elegantissima , which are abundant on intertidal rocky shores , and which eat a variety of zooplankton, including those with strong escape responses such as copepods . In this study we used calanoid copepods as model prey organisms because they are an important component of the diets of many benthic suspension-feeding organisms , and because their swimming behavior in response to various conditions of flow is well-characterized . We examined how the turbulent and wavy flow observed in shallow coastal habitats affect encounter, capture, and retention rates of zooplanktonic prey by a passive suspension-feeding sea anemone. Our goal was to compare the effects of turbulence and waves on predator-prey interactions between passive suspension feeders and actively-escaping zooplanktonic prey with the effects of similar ambient flow on interactions between benthic fish and such prey. All individuals of Anthopleura elegantissima were collected from Horseshoe Cove, in the Bodega Marine Reserve along the Sonoma Coast in California , during October 2012 and May 2013. Sea anemones from one clone were gently peeled from the rock using a butter knife, and each individual was placed in a separate plastic bag filled with air. The bags were kept in a cooler at 10- 15°C and transported to the University of California Berkeley . The anemones were maintained for ten days in a 19-liter aquarium where they were placed on a suspended plastic mesh substratum to prevent attachment to the aquarium walls. In a temperature-controlled cold room kept at 10-15 °C, the aquarium had recirculating filtered seawater with a salinity of 35‰.

The sea anemones were exposed to a photoregime of a 12 hours dark and 12 hours light provided by full-spectrum fluorescent bulbs . Sea anemones were fed hatched Artemia spp. nauplii once a day, but were not fed 24 hours before use in flume experiments. For flume experiments, sea anemones were transported to the University of North Carolina Wilmington via overnight delivery. Individual sea anemones were placed in plastic bags that were filled with oxygen. The bags were packed into a Styrofoam cooler over a base of ice packs and a middle cushioning layer of newsprint. Upon arrival sea anemones were removed from the plastic bags and housed under aquarium conditions identical to those previously described. Zooplankton were collected from the Bridge Tender Marina in Wilmington, North Carolina , using a plankton net . Samples were diluted in seawater, aerated, and used within 12 hours of capture. Individual calanoid copepods, Acartia spp., were selected using Pasteur pipettes, and held in beakers with bottoms made of Nitex mesh that were submerged in filtered and UV-treated seawater. Before experiments, copepods were dyed red to make the organisms easy to visualize in videos. To dye the plankton, the mesh beaker was submerged in a solution of Neutral Red for 20 minutes . Copepods were videotaped while swimming in still sea water at 15°C in an aquarium before and after being stained. The trajectories of the copepods were digitized with ImageJ , and the behaviors were categorized and measured using Python .Swimming speed, duration, and direction measured from copepod trajectories in still water were not significantly different between undyed copepods and dyed copepods . For control experiments that used dead prey, copepods were heat-shocked after the dye treatment. Laboratory experiments using an oscillating flume were conducted at the University of North Carolina Wilmington. A motor-controlled piston drove FSW back and forth through a U-shaped flume with a sealed working section that was 50 cm long, 10 cm wide, and 10 cm tall . In some cases copepods were captured on the far side of the observed tentacles. If a copepod carried in the flow “disappeared” behind an illuminated tentacle and did not re-emerge, we assumed that it was captured. When this occurred, the tentacles were observed carefully in subsequent frames of the video and in every case the captured copepod became visible when the tentacles moved, the copepods fluttered into view during peak velocities, or the copepods washed off the tentacles. In addition, aerial-view photos of each sea anemone in still water were taken directly after the experiment and captured copepods were noted. No discrepancies occurred between the total number of captured copepods counted by the end of the experiment and copepods observed on the tentacles once the experiment was complete. To quantify the vertical distribution of copepods in the water column, and thus the relative availability of prey in the sea anemone’s capture zone, a distribution ratio was calculated for prey in strong and weak wave regimes. The number of copepods per time that passed through the area above a sea anemone was counted in each video . The ratio described the rate at which swimming copepods passed above the copepod in the ambient flow, relative to the rate at which swimming copepods were carried through the capture zone.

My own combination of these three fields would not be possible without thespaces already opened by those mentioned above. As a final opening thought, I note that anthropologists and social scientists involved in contemporary productions must consider the consequences of collaboration. And they must attend to the reflexive modes that are engendered within and between institutions and disciplines. If “the essence of tyranny is the denial of complexity,” then we must also consider the question, what sort of tyrannies are perpetuated by the institutionalization of interdisciplinary complex systems approaches?This attention to and tension around the internalization of social science in the living laboratory of The Bahamas runs through this dissertation and through my own participation in scientific productions there, and it was the feeling of this tension that started me on the path to what would become this project. In the summer of 2002, long before this dissertation was conceived of, I traveled to The Bahamas for the first time to conduct research towards the completion of my undergraduate thesis in environmental biology. Out of several ongoing projects from which biology students were to choose to participate as a project assistant, I chose to join the American Museum of Natural History’s Bahamas Biocomplexity Project and their initial attempt to administer socioeconomic surveys in fishing communities in The Bahamas. I was told that this social aspect of the project would be integrated,ebb flow table after a period of years, with regional biological and environmental data in order to put together a systemic model of the relationship between local human populations and the regional marine ecosystem functioning in order to inform policy on the creation and management of a proposed marine reserve network .

It was my questioning of this notion of the possibility and promise of “integration” and scientific holism that eventually inspired my own collaborations in The Bahamas, presented here.The arena of Caribbean Studies is one example of critical scholarship which interrogates social and historical categories and forms. I engage with this work throughout this dissertation in order to consider how we might think of the laboratory of The Bahamas today and how we might come to experiment in and inhabit the world. And yet an analysis of the living laboratory of The Bahamas does not flow easily from Caribbean Studies, and this is precisely because The Bahamas both is and is not Caribbean, and because the familiar objects and orientations of Caribbean social science might not adequately speak to some of what is happening there in the contemporary moment. My work in The Bahamas has taught me about the politics of being Caribbean. “Caribbeaness” is a complex attribution with which The Bahamian state and Bahamian people grapple with continually. Historically, The Bahamas has been subject to the same wide ranging and influential events as the rest of the Caribbean region, most notably the transatlantic slave trade, European colonialism, and the 20th Century independence movement. And yet, The Bahamas has been excluded from many collections of social science on the Caribbean and is usually not listed as a Caribbean country when scholars discuss the countries of the region, though it is often categorized as part of the Caribbean Region when it comes to international state politics. For example, the United States’ Central Intelligence Bureau lists it as a Caribbean nation. This confusion results from more than the fact that The Bahama Islands are not in the Caribbean Sea . It has been written that Bahamians do not consider themselves Caribbean because their affinities and trade ties lie more with the US than with the other islands.It has also been written that The Bahamas, due to its long history of success with tourism, is too wealthy to be classed with the rest of the Caribbean, or even the Caribbean of former British colonies.

The Bahamian government has reservations about its membership with the Caribbean economic community and its subsequent inclusion in the Caribbean free market. In this vein, I am interested in the ways in which The Bahamas does and does not exercise its “Caribbeanness,” and I cannot begin with the analytic assumption that this is a Caribbean place, even if these islands share a Caribbean history. This observation has necessitated an investigation into Caribbean Studies and Caribbean Anthropology in order to gauge how to relate this living laboratory to the discipline’s themes, conversations, and tensions.The social science literature on the Caribbean is extensive and diverse, and throughout the 20th Century development of Caribbean Studies the Caribbean area has become a specific “testing ground” for social scientific research and a metaphoric representation of evolving social forms. Through the exposition of case studies, the delineation of social models, and the evocation or refutation of sociological and anthropological problems and conceptual orientations, The Caribbean has provided ground for the production and deconstruction of such notions as cultural contact, New World society, class solidarity and diversity, systems of global production, colonial history, ethnicity, race, religion, gender, nationalism, transnationalism, diaspora, identity politics, globalization, creolization, paradise, and modernity- much of this scholarship under the rubric of colonial/postcolonial studies which variously tackle the theorizing of the practices and politics of oppression and resistance. The particular contingencies of specific Caribbean places have come, variously and inconsistently, to stand for general truths about kinds of postcolonial human nature, or their refutation and/or the nature and practice of postcolonial social theory itself. It is not a stretch to say that the Caribbean has come to be understood as a sort of living laboratory for colonial and postcolonial social research. Yet, during my time in The Bahamas I encountered processes, specific events, and situations that the academic genealogy of Caribbean social science cannot quite speak to because there are many processes at work simultaneously economic, biological, anthropological, and more. This creates a situation which forces one to create cross-cutting conceptual combinations in order to tell new stories and to ask new questions which may or may not be deemed postcolonial, but which owe a debt to this scholarship in any case.

David Scott’s work provides a sense of reading diverse literatures together, and he captures how one might successfully work with postcolonial studies and build off it to create a new orientation. Antonio Benitez-Rojo’s work speaks to a postmodern understanding of the Caribbean, tracing the islands as a form of thought, discussing the mystery, ambiguity, and dynamism the region has historically presented to the world.Scott has a complex approach to the consideration of the postcolonial contemporary Caribbean. His is a critique of those authors who seek to re-imagine the colonial past in the hope of altering the present, and he notes that little consideration has been given to what it is about the present which necessitates revising the past. He writes, “the precise nature of the relation between pasts, presents, and futures has rarely ever been specified and conceptually problematized. It has tended, rather, to be assumed, to be taken for granted.”Scott notes that most postcolonial Caribbean critiques, such as those criticisms of various forms of anticolonial nationalism, take up the goals of nationalist movements,hydroponic grow table and explain how they have failed, as answers, in the present. What these critiques don’t do, however, is consider the problems that the anticolonial nationals constructed in the first place. They merely assume that the colonial problems then, classic Fanonian problems of colonial racism and oppression, are the same as the postcolonial problems now. This, for Scott, tends to lead to the exposition of the negative structures of colonial power and to the concomitant narrative description of a romanticized subaltern agency in the face of this negating power. Scott’s view is different: “it is our postcolonial questions and not our answers that demand our critical attention.” In order to rethink postcolonial Caribbean questions, Scott arrives at the conception of the temporal problem-space. This is the discursive context of dispute and intervention around which questions, answers, and stakes are posed, and this is related to the notion that criticism within a problem-space, Scott’s own goal, must be strategic and alert in order to determine whether the“questions it is trying to answer continue to be questions worth having answers to.” Such criticism poses new hope for the proposition of political alternatives in our present and for the imagination of possible futures because the re-conception of the problem opens new space for the conception of possible responses. Scott’s main example in his monograph is C.L.R. James’ The Black Jacobins, the famous anti-colonial and epic narrative of the Haitian Revolution and the tragedy of Toussaint L’Ouverture. Tragedy, Scott notes, problematizes the “view of human history as moving teleologically and transparently toward a determinate end, or as governed by a sovereign and omnisciently rational agent.”

Tragedy raises doubts about the relation between pasts, presents, and futures, it exposes the “hubris of Enlightenment and civilization” and points toward a more complex and contingent understanding of human life.With such a conceptual view of tragedy and problem-space in mind, Scott hopes to reread The Black Jacobins as a work which moved beyond the anti-colonial, a work which provides grounds with which to critique the postcolonial present. In a meditation on modernity, Scott discusses critiques of James as unaware of the diversity within modernity, stating that the Enlightenment idioms promoted by the French Revolution were an important aspect of Toussaint’s revolutionary subjectivity and that to worry otherwise is to miss the point that subaltern resistance is no longer at stake in the way that it was. The relevant questions for Scott concern the problem of modernity, understood in the Foucauldian sense of a positive formation of power that shapes the material and epistemological conditions of thought and possibility. Toussaint L’Ouverture, in this schema, becomes a conscript of modernity, not only a resisting agent. The plantation is also reconsidered in this view as a form of modern power which shaped conditions of slavery and subjectivity, and this moves the consideration of slavery away from the anti-colonial criticisms of its negative effects and the search for agency. He notes that “what is at stake here is not whether the colonized accommodated or resisted but how colonial power transformed the ground on which accommodation or resistance was possible in the first place, how colonial power reshaped or reorganized the conceptual and institutional conditions of possibility of social action and its understanding.”Thus, for Scott, Toussaint is a conscript of the founding modernity of the Caribbean, a founding modernity that continues to shape the thoughts and lives of others in the region. The lack of a visible indigenous population in the Caribbean, and the forced and brutal “civilizing”process of plantation slavery, make the Caribbean the inaugural form of modernity. In the plantation, slaves and masters were altered in modern ways and inserted into modern global processes that would come to matter for reasons because of their dehumanization and violence. The point is, for Scott, that the Caribbean put forth new conditions of life, creating the West Indian as the conscripted subject and object of a modern ethos. But how do we describe the contemporary ground that shapes these conditions of life in the Caribbean today? How do we characterize the current confluences of productivity that create the region as a particular kind of problem space? Benitz-Rojo has a complex framework for nonreductive thinking about the region which I find helpful as a frame for the discussion to follow. His analytic mode of “Chaos,” referring to the advent of disorder in the passage of time, nonetheless has an emphasis on repeating dynamic states and regularities. He writes, “I have tried to analyze certain aspects of the Caribbean while under the influence of this attitude, whose end is not to find results, but processes, dynamics, and rhythms that show themselves within the marginal, the regional, the incoherent, the heterogeneous, or, if you like, the unpredictable that coexists with us in our everyday world.” The trope of repetition, within this mode is especially salient for Benitez-Rojo, because only repetition as difference, the motion of irreducible change, can be identified in the fluidity of Chaos that is the sociocultural Caribbean.

While DCA and INA behave similar in nahG plants, these two compounds differ profoundly in their level of dependency on the transcriptional co-factor NPR1 . Although the defense inducing activity of INA is fully blocked in npr1-3 plants, DCA is only partially reduced in this mutant. Thus, with CMP442, DCA and INA a small set of synthetic elicitors is now available that has different activating effects on the SA-dependent plant defense network . These molecular probes along with additional synthetic elicitors from our screen and genetic mutations are likely to prove highly useful for the fine dissection of this complex regulatory network.Chemical pesticides currently in use typically rely on direct antibiotic or biocidal activity, which often leads to undesirable toxic environmental side effects . In response to these concerns the U.S. Environmental Protection Agency has established a program to facilitate registration of new reduced-risk pesticides that have a reduced impact on human health and other non-target organisms . Synthetic elicitors identified by our project protect plants by inducing their natural immune responses. As their primary mode-of action does not involve the inhibition of key metabolic or developmental steps in target organisms, they are likely to be less harmful for humans and the environment than conventional pesticides. Due to the continuous pollution of the environment caused by the massive use of traditional pesticides and the increasing awareness of environmental protection issues of consumers and farmers in the US, Europe and other parts of the globe,vertical grow system innovative “green” pesticides suitable for conventional farming practices are urgently needed.

A possible disadvantage of the use of synthetic elicitors for crop protection is that permanent defense activation often results in fitness costs, due to the phytotoxicity of some defensive plant products and resource allocation away from growth or reproduction. For example, as a result of its long-term activity, the synthetic elicitor 2,6-isonicotinic acid , which was developed in the 1990s by Ciba Geigy, was insufficiently tolerated by some crop plants to warrant practical use as a plant protection compound . However, we found DCA and CMP442 to be promising in this respect when contrasted to other known defense elicitors, such as INA or BTH , their defense-inducing activity is only transient and weakens within several days after application . In addition, low doses of CMP442 proved to be beneficial for plant growth. Arabidopsis and tomato grown on solid medium containing low concentrations of CMP442 developed significantly longer roots than untreated seedlings. In addition, single root drench application of CMP442 enhanced growth of aerial parts of soil-grown Arabidopsis and tomato. Thus, CMP442 appears to be uniquely suited to provide plant seedlings with both protection from diseases and enhancement of vigor. We also found several other synthetic elicitors, including DCA, that have similar effects on root growth at low concentrations. However, of those synthetic elicitors we tested so far CMP442 is the most efficient one in this respect. CMP442 strongly enhanced growth of Arabidopsis roots at a concentration of 1 µM. At this concentration CMP442 still can induce defense responses.As shown in Figure 2.3, 10 µM of CMP442 was sufficient to significantly suppress the development of HpaNoco2 spores in Arabidopsis. Despite these promising observations, further studies are needed to explore the full potential of CMP442 for simultaneous disease protection and growth enhancement for crops.

Several regulatory proteins were found to contribute to both defense and developmental processes . These include the Arabidopsis proteins SGT1b, AS1 and AtTIP49a . For example, SGT1b, a regulatory component of SCF complex ubiquitin ligases, was found to be involved in controlling stability of several R proteins as well as the activation of ETI, but also SCFTIR1-mediated auxin responses, such as root development and apical dominance . We recently reported that Enhanced Downy Mildew 2 , which is required for R-mediated resistance of Arabidopsis against the Hiks1 isolate of Hpa, positively affects floral transition . EDM2 has additional roles in plant development, such as promoting proper leaf pavement cell development and controlling the succession of leaf types formed during early vegetative stages of Arabidopsis. An increasing number of studies are reporting on similar molecular links between plant immune and developmental processes. The molecular nature and biological purpose of crosstalk between both types of processes is poorly understood at this point. CMP442, with its clear effects on both plant immunity and growth, is likely to serve as a valuable tool for the dissection of molecular crosstalk between defense and development. We are currently testing its effects on both defense induction and growth enhancement in a variety of known Arabidopsis signaling mutants. Results from these and related studies should shed light on the fascinating, but yet enigmatic, link between seemingly unrelated types of physiological processes in plants. CMP442 may also allow for the discovery of fundamental causes of the general phenomenon of hormesis. Although widely described for numerous types of organisms and physical, chemical or biological stimuli, the genetic and molecular basis of hormesis is largely unknown.

Hormesis is characterized by a biphasic dose-response to a treatment which stimulates at low doses and has an inhibitory or toxic effect at higher concentrations . Biologically, hormesis is believed to be an adaptive response at either the cellular or organismal level to stress. The exposure to low doses of herbicides to produce enhanced growth has been widely reported on . Recent research has revealed some signaling pathways and mechanisms that are responsible for specific hormetic responses. These involve certain ion channels, protein kinases, deacetylases, transcription factors, chaper ones, antioxidant enzymes, and glutathione peroxidase . Another noteworthy observation is that some inducers of hormetic responses can protect the respective cells or organisms against a variety of additional stressors later on . Although the phenomenon of hormesis has been known for several decades, our knowledge of its biological basis is fragmentary at best and much remains to be explained. In particular, it is unclear if the great variety of hormesis-like phenomena have a common functional basis, or if they are mechanistically unrelated. A comprehensive comparison of molecular responses triggered by a variety of hormesis-inducing stimuli in a single type of organism, such as the versatile molecular genetics model Arabidopsis, may allow defining common denominators for this complex phenomenon. Plant diseases can be caused by pathogens with different types of lifestyles. While biotrophic pathogens require living host tissues to complete their life cycles, necrotrophs feed off dead plant cells. The phytohormones salicylic acid , jasmonic acid , and ethylene are known to coordinate plant defense responses to combat the respective type of infecting pathogen. Currently, most documented interactions between JA- and SA-dependent signaling processes are antagonistic, but their interactions are complex and details of crosstalk between them are not fully understood. Upon recognition of necrotrophs, an increase in JA and ET synthesis occurs along with enhanced transcript levels of defense genes, such as Plant Defensin 1.2 ,mobile grow system which is often used as a marker for induction of the JA pathway. Plant defensins are small peptides that can be found throughout the plant kingdom and are encoded by small gene families. Here I report on the development of a screening procedure to identify synthetic elicitors that activate the JA-/ET-dependent branch of the defense network. Towards this end, a set of genes was identified that display SA-independent upregulation in response to infection with the biotrophic oomycete Hyaloperonospora arabidopsidis . Four of the five genes are PDF members including PDF1.2b. Additionally, efforts to create Arabidopsis thaliana lines containing RNA silencing transgenes cosilencing closely related PDF family members are described. Plants are constantly assaulted by a variety of biotic stressors, such as microbial pathogens. Most pathogens are unable to infect plants, making disease the exception, not the rule . Plant pathogens are typically divided into two main categories: biotrophs, which obtain nutrients through living tissue and necrotrophs, which must kill plant tissue to acquire nutrients .

Plants evolved the ability to recognize pathogens and tailor their defense responses to the type of infecting pathogen . They possess an inducible immune system enabling them to specifically recognize molecular features of pathogens and activate transcriptional cascades defending the plant from disease . When these mechanisms are absent or inactivated by pathogen effector molecules, plants are rendered susceptible . Pathogen effectors are proteins or small molecules secreted into host cells that attenuate defense signaling processes weakening plant immune responses. Strong immunity against pathogens can be mediated by plant disease resistance genes, which encode receptors that specifically recognize effectors from distinct pathogen races . Thus, such race-specific immunity is based on interactions of complementary R– and effector-genes . A hallmark of R-mediated disease resistance is the hypersensitive response , a programmed form of plant cell death localized to pathogen infection sites. HR is an effective defense reaction against biotrophic pathogens, which are dependent on live plant tissue . During compatible interactions, basal defense is activated, which is a weakened form of plant immunity that does not involve HR and is typically insufficient to prevent disease . R-mediated disease resistance is frequently facilitated through the SA-dependent branch of the defense network, which is often attributed to defense responses against biotrophic pathogens whereas the JA- and ET-dependent mechanisms seem preferentially to mediate immunity against necrotrophs Thus, the plant immune system is able to specifically tailor distinct responses against different types of pathogens. Fine tuning of these responses is mediated by complex crosstalk between individual signaling branches . The timing, amplitudes and spatial distributions of certain defense signals determine the individual defense reactions activated in response to a given type of pathogen. One pathogen widely utilized to study plant defense is Hyaloperonospora arabidopsidis , an oomycete and obligate biotroph known to exclusively infect the model plant species Arabidopsis thaliana. The study of this pathosystem has facilitated the identification of more gene-for-gene interactions than any other plant and pathogen combination . Thus far, SA-dependent defenses have been directly attributed to limiting Hpa growth in this pathosystem with JA/ET having no distinguishable role . The majority of plant disease research indicates that interactions between JA- and SA-signaling are antagonistic, although it has also been demonstrated that at low concentrations they can act synergistically . JA is a lipid-derived signal that has many vital roles in plants . Responses to JA are controlled by a regulatory apparatus consisting of four key components: the JA signal, the ubiquitin ligase SCFCOI1, the jasmonate ZIM-domain repressor proteins, and transcription factors that positively regulate expression of JA-responsive genes . JA-signaling is involved in complex processes such as pollen maturation, response to wounding, fruit ripening, root growth, and even tendril coiling . The role of JA in the defense response to insect wounding was first suggested in 1992 . JA- and ET-dependent regulatory processes can act cooperatively . For example, both JA- and ETsignaling contribute to resistance against necrotrophic pathogens and are knownto inhibit the formation of HR. This dual function is advantageous for the plant, since necrotrophs feed off dead tissue and may benefit from HR . Activation of JA-mediated defenses are preceded by the accumulation of jasmonates synthesized by the octadecanoid pathway . However, knowledge of the JA-signaling pathway is still incomplete. Differences exist between the JA-signaling systems studied in different plant species. For example, although the system in pathway induces systemic JA responses in tomato, no evidence has yet indicated such a pathway exists in Arabidopsis . When some plants are subjected to predation, the JA pathway is activated, requiring a 200-amino acid precursor, prosystemin. Prosystemin then produces the 18-amino-acid peptide, system in, through proteolytic processing . Systemin induces the production of H2O2, followed by the biosynthesis of JA and leading to the activation of defense-related genes . The first steps of JA biosynthesis occur in the chloroplast where membrane-derived linoleic acid is converted to 12-oxo-phytodienoic acid using multiple biosynthetic enzymes . OPDA is then transported to the peroxisome, where it is reduced to OPC-8:0 by OPDA reductase3 undergoing three rounds of β-oxidation, resulting in the production of -7-iso-JA . Studies found that a main bioactive form of JA is JA-isoleucine , which is produced by conjugation of JA to Ile by Jasmonate Resistant 1 .

Tropical and arctic ecosystems are largely under sampled. Moreover, the PFT-based root distributions have not been updated accordingly. A global-scale maximum rooting depth data set was synthesized by Canadell et al. [1996] and included 253 plant species. They also aggregated maximum rooting depth data based on PFTs, which is readily applicable to large-scale land models. The rooting depth followed the order: forest > shrub > herbaceous plants > – crops. However, within-PFT variation was quite large. For example, the maximum rooting depth of tropical species was 68 m, while the mean of tropical evergreen plant maximum rooting depth was about 15 m. Particularly for arctic tundra, a more detailed rooting depth data set was developed by Iversen et al. [2015a]. Tundra maximum rooting depth ranged from 0.7 cm for a deciduous shrub species to 100 cm for a forb species . In general, evergreen shrub tundra has the shallowest rooting depth . Grass, forb, and deciduous shrub tundra have deeper root systems , and sedge tundra has the deepest roots . This data set casts doubt on land model PFT classifications for arctic tundra. For example, CLM and ALM represent arctic tundra with only two PFTs , which substantially under represents root traits across the wide range of dominant tundra species, including arctic grasses, sedges, forbs, deciduous shrubs,nft hydroponic and evergreen shrubs [Chapin et al., 1996].The ability of plants to recognize and respond to the presence of threats is vital for their survival. Given their sessile lifestyle this defense response must be swift.

Major threats to plants include diseases caused by microbial phytopathogens. Evolution has duly equipped plants, resulting in plant disease being the exception, not the rule . However, due to extensive selective breeding and the tendency of farmers to plant monocultures, plant disease has gained a foothold and has become a multibillion dollar problem . Currently, the solution is the application of pesticides which are often not only toxic to pathogens but can affect non-target plant and animal species . The off-target effects of pesticides make the discovery of novel solutions to the plant disease problem crucial . In plants, many physical and chemical barriers exist that passively prevent pathogen infection. Physical barriers can include: a waxy cuticle, stomata, and thick cell walls. Chemical barriers include phytoanticipins, phenolics, and quinines which have antimicrobial properties, as well as lactones, cyanogenic glucosides, saponins, terpenoids, stilbenes and tannins . While passive defenses are effective against some phytopathogens, an active immune system is required to combat pathogens able to bypass passive immunity . One such form of active defense includes small basic peptides called plant defensins . PDFs can interfere with a pathogen’s ability to extract nutrients, thus delaying pathogen development . Plant-pathogen interactions are dynamic and shaped by a ‘coevolutionary arms race’ . In this arms race, there are strong selective pressures for the plant to maintain its resistance against a given pathogen, as well as pressures on pathogens to overcome plant defenses . Like mammalian organisms, plants possess an inducible innate immune system that is based on the genetically determined and inheritable recognition of molecular features of pathogens .

Unlike mammals, however, plants do not have specialized immune cells and most plant cell types are capable of efficient innate immune responses. In addition to local innate immunity acting in plant tissues subject to pathogen attack, mobile signals generated in such primary infection sites control systemic defense responses mediating long lasting broad spectrum disease resistance. This innate immune system is constantly evolving in a fashion described by the ‘zigzag model’ . According to this model, the most fundamental form of plant innate immunity involves recognition of conserved molecular signatures shared by many classes of pathogens termed microbe-associated molecular patterns . MAMPs are recognized by pattern-recognition receptors on the surface of plant cells. MAMPs are essential for a pathogen survival and fitness and cannot be discarded or altered through evolution to evade PRRmediated detection . Examples of MAMPs include: chitin and ergosterol from fungi, β-glucans from oomycetes, fungal xylanase and oomycete transglutaminase, as well as flagellin and lipopolysaccharides from gram-negative bacteria . Upon recognition of a MAMP, the plant activates a comprehensive set of defense reactions called pattern-triggered immunity . During PTI there are extensive molecular, morphological, and physiological changes . Signaling cascades link recognition and response. Within minutes of MAMP recognition, there are ion fluxes across the plasma membrane, an increase in cytosolic Ca2+, an oxidative burst, which includes the production of reactive oxygen species and nitric oxide, MAP kinase activation, protein phosphorylation, and receptor endocytosis . Protein kinases are major regulators of plant defense responses that act at various hierarchical levels within the defense network . There are more than 1000 protein kinases in the plant model organismArabidopsis thaliana . In particular, receptor protein kinases , Ca2+ dependent protein kinases and MAPKs have been extensively implicated in the regulation of plant immune responses. The plant immune responses are controlled by a complex regulatory network consisting of multiple interconnected sectors that include those regulated by salicylic acid – and others dependent on jasmonic acid and ethylene as well as other less well characterized pathways .

Over time, pathogens evolved effector molecules which are released to augment virulence by manipulating and weakening, PTI resulting in effector triggered susceptibility . Such interactions between virulent pathogens and susceptible plants are termed “compatible”. A susceptible plant still maintains low levels of defense, called basal defense. Basal defense is not sufficient to fully prevent disease, but it can slow its progression . PTI is often successful against pathogens that have not evolved the ability to specifically infect a plant; this is referred to as non-host resistance. To counteract ETS, plants evolved resistance proteins , which specifically recognize pathogen effectors resulting in a resistant plant and an avirulent pathogen . This type of innate immunity is referred to as effector-triggered immunity . ETI is a faster and more robust version of PTI,nft system and often results in a hypersensitive response at the site of infection . HR involves a programmed form of death of plant cells directly in contact with an invading pathogen. In some cases pathogens evolved additional effectors to evade ETI . ETI is active against adapted pathogens. Although, these relationships are not always set in stone and they may depend on the specific elicitor molecules present during pathogen infection .This means that they can recognize pathogen effectors if tge effects of the effector on the host target. A strong oxidative burst and HR cell death are considered hallmarks for resistance mediated via R genes. ROIs have antimicrobial properties and act as a signal for activation of defense responses, including HR . HR cell death is an efficient immune response against biotrophic pathogens . Biotrophic pathogens extract their food from living plant tissue, while necrotrophs kill and digest dead plant tissue for their nutrients. Thus, by decreasing the number of cells in contact with an invading biotrophic pathogen, plants can prevent further infection. Basal defense and some cases of ETI are controlled by the SA-dependent branch of the defense network . The molecular changes that occur after pathogen recognition during ETI also occur during compatible interactions, but with ‘slower kinetics and reduced amplitude’ . SA-dependent signaling processes involve several genetically defined defense regulators, such as EDS1 and PAD4 , which control the synthesis and accumulation of this defense hormone. Defense associated SA appears to be mainly synthesized by a plastidic pathway that involves isochorismate synthase 1, which is also known as EDS16 or SID2 .

Elevated SA levels activate a set of downstream defense responses, such as expression of pathogenesis-related genes and HR cell death . A positive feedback loop links ROI, NO and SA . These signaling molecules mutually control their production. Only strong activation of this feedback loop results in the induction of HR cell death . Typically levels of ROI, NO and SA accumulation during basal defense are too low to trigger HR . Sifficiently high levels of these signaling molecules for HR induction are typically observed during ETI . SA is also a critical signal for the activation of systemic acquired resistance , a broad-spectrum defense response that is sometimes activated throughout the entire plant in response to local recognition of either virulent or avirulent pathogens . The main role of SA in SAR induction seems to be in the systemic tissue, where it causes the transcriptional co-activator NPR1 to move from the cytoplasm to the nucleus where it interacts with transcription factors, activating SAR . The SA-derivative, methyl salicylate , acts in tobacco as a long-distance mobile signal for SAR within the plant . In addition, MeSA can also serve as the airborne signal that induces defense gene expression in neighboring plants . Recent studies have revealed that SAR can increase the fitness of pathogen-challenged plants in a field setting . Although constitutive activation of SAR has substantial fitness costs . R proteins do not confer resistance against necrotrophic pathogens, which kill plants and feed off dead host tissue. Defense against necrotrophic pathogens is mediated through the jasmonate acid and ethylene branches of the defense network. The JA/ET branches are also known to have roles in responses to wounding and herbivore attack . The SA, JA, and ET pathways interact extensively. A large body of research has indicated that SA and JA are mutually inhibitory . Recent evidence indicates that they may enhance each other’s expression at low concentrations . A plant must be able to distinguish between different types of pathogens allowing it to respond with an appropriate set of defense reactions, mediated by signaling molecules. Thus, different signaling mechanisms are required to activate immune responses against pathogens with different life-styles. Studies indicate that while sometimes ET and JA interact synergistically in disease responses, that both can act independently or even antagonistically with the SA-dependent pathway . Resistance to specific pathogens conferred through JA signaling show little overlap in transcriptional changes. This context is important to fine-tuning the JA response . ET and abscisic acid regulate different branches of the JA response . JA and ET act together to induce the expression of PDF1.2 . The transcription factors, ERF1 and ORA59 work to integrate JA and ET signaling . These transcription factors confer resistance against necrotrophs . Alternately, MYC2 works with ABA signaling to negatively regulate the JA-ET responsive branch while activating genes within its own branch, such as VSP2 . This branch is associated with the wound response and priming for pathogen defense .Arabidopsis and the oomycete, Hyaloperonospora arabidopsidis , are an effective model pathosystem in which defined R-genes mediate recognition of certain Hpa isolates . Well characterized Arabidopsis mutants allow for the fine dissection of defense pathways . While useful, traditional genetics techniques are unable to circumvent functional redundancy and lethal phenotypes. This suggests that additional experimental approaches are necessary to advance knowledge of mechanisms controlling plant immunity. Chemical genetics/genomics offers distinct advantages over traditional techniques through the use of small molecules, whose effects are often impermanent and reversible. Small molecules also provide more defined temporal control. In contrast, the timing of pathogen infections is not easily defined, as the germination of spores or pathogen growth and spread in plants is often asynchronous.As discussed above, different plant species have developed effective mechanisms to cope with pathogens. Unfortunately, contemporary crops have lost parts of their innate immune system due to breeding efforts focused mainly on increasing yield. Consequently, plant diseases cause dramatic losses in crops every year. In the United States 500 million kg of pesticides are applied annually at a cost of $10 billion to farmers to control disease. Despite this, more than a third of all food crops are still destroyed by diseases . The lingering residues of pesticides on produce is currently a major health concern of consumers . Many pesticides currently in use are carcinogenic and rely on direct anti-pathogenic activity, which often leads to undesirable side effects that can have far reaching consequences both for humans and the environment . This disquiet over the dangers of pesticides has spawned considerable interest in alternative methods of disease control .

Therefore each set of R genes incorporated into a cultivar must be evaluated systematically requiring a significant investment of time. However, it is clear that gene pyramiding offers an attractive mechanism for combining the individual specificities of R genes as well as taking advantage of their synergistic effects to generate broad-spectrum resistance.An alternate strategy to breeding is to directly introduce a cloned resistance gene into a plant via transgenic technology. Introduction of a gene by transgenic means can overcome the limitations of traditional breeding, namely inter species sterility. Additionally, transgenic technologies allows multiple genes to be inserted simultaneously. However, validation of the function of the transgene and its stability and heritability after transformation requires a significant investment of time and resources. Further, the transgenic lines must also undergo subsequent analysis for agronomic traits before release. While the creation of transgenic plants may be relatively straightforward for a number of species, the strategy has its own substantial time requirements. The greatest advantage of transgenic technology is its ability to overcome fertility barriers for the dissemination of genes originating from a different species; two examples from the Solanaceae family highlight this advance. Bs2, as mentioned above, was identified originally in pepper and its resistance has been durable in the field against isolates of X. campestris . Due to the fitness requirement associated with avrBs2 locus,ebb flow tray the incorporation of the resistance locus Bs2 via transgenic technology may offer durable resistance in a number of plant systems affected by X. campetris.

To assess this hypothesis, tomato was transformed with the Bs2 gene from pepper. Inoculations of X. c. pv vesicatoria isolates onto Bs2– containing transgenic tomato plants failed to cause disease therefore Bs2 function was conserved in tomato . Tomato and pepper when crossed cannot form a fertile hybrid and this resistance could not have been utilized with standard breeding protocols. In another example the N gene from tobacco, conferring resistance to the tobacco mosaic virus , was transferred into tomato . The resulting transgenic tomato plants, expressing the N resistance gene, were inoculated with TMV and complete resistance was observed. While TMV is not as devastating economically to tomato as is X. campestris, the conceptual notion that resistance loci can be transferred among species while retaining their function points illustrates a key advance for engineering resistance using transgenic technology. These examples demonstrate conservation in disease signaling pathways that can be exploited for cultivar improvement.Disease resistance research has largely focused on understanding the specific pathogen–host interactions mediated by R and avr loci. Recently, studies have revealed signaling components that function downstream of R genes or other pathogen sensors. Studies on broad-spectrum resistance pathways, such as the rhizobacteria-mediated, induced systemic resistance pathway and the insect-responsive pathway involving jasmonic acid are rapidly gaining momentum . However, research on the pathway transducing a broad-spectrum defense response termed the systemic acquired resistance response has progressed most rapidly. Chemical and abiotic inducers of SAR, along with inherent signaling components of this pathway identified by basic research in model plant systems, are among the initial targets being used to engineer multi-pathogen disease resistance in important crop plants.

The SAR defense response is manifested when a plant host is inoculated with a pathogen that results in a localized infection. This primary infection subsequently primes the host to resist secondary infections by viral, oomycete and bacterial pathogens . In the model plant Arabidopsis, SAR is associated with a rise of internal levels of the plant hormone salicylic acid , and is correlated with the increased expression of a set of genes termed pathogenesis related genes . Several PR genes encode proteins with antimicrobial activity and thus contribute to an overall defense response directly . Research aimed at modulating this pathway and generating broad-spectrum resistance has largely targeted three parts of this response for further study: the ability of SA to trigger the response, the increased expression of PR genes and the identification and modulation of other signaling components.Therefore, investigations into the costs of induced resistance have started by assaying the effects of using chemical inducers. Heil et al. have studied the fitness of wheat plants treated with BTH in the absence of pathogens. When plants were grown either hydroponically or in the field, water-treated control plants were able to achieve greater biomass than their BTH-treated cohorts. In field experiments, however, significant growth differences were not seen until approximately 6 weeks after treatment. The authors suggest that many of the potential fitness costs associated with induced resistance responses may be masked in laboratory experiments where growth conditions are kept optimal, and support this hypothesis with experiments performed growing plants under differing nitrogen concentrations. In addition, when the age of the plants induced for SAR was considered it was found that the growth-costs of BTH treatment could be reduced if the BTH was applied after the lateral shoot formation was complete .

These data also underscore the importance of factoring plant developmental programs into any efficient strategy to enhance plant resistance by chemical treatment or genetic engineering.Another unwanted effect that may arise from transgenic manipulation of genes involved in defense signaling pathways is spontaneous cell death. Spontaneous cell death has been uncovered in many genetic screens for enhanced disease resistance and recently, has been seen in transgenic plants. These mutants and transgenic plants are often collectively referred to as lesion-mimic mutants since they display lesions similar to those observed in a defense response even in the absence of pathogens. This form of cell death in plants is sometimes influenced by alterations in environmental conditions such as light, temperature and humidity . Therefore, both in basic research and in applied experiments, it will be important to understand the parameters controlling cell death. This research is critical not only for optimizing the situations where transgenes and chemicals will be most useful to generate disease resistance, but also to minimize negative effects on important agronomic factors such as development, fertility and yield.Many of the examples listed above,flood and drain tray may appear as substantial challenges to engineering disease resistance, however, these challenges provide opportunities to create plants that are even more resistant than plants engineered based on our current knowledge. For instance if the already identified components of a signaling pathway are not the best candidates for durable resistance in the field, technologies such as micro-arrays will help to pinpoint novel targets of interest . When mutations involved in disease resistance have already been identified, but are recessive in nature such as the mlo, edr1 and mpk4 mutants, classical breeding strategies can be employed. These mutants cannot be placed into heterologous systems using transgenic technology but, as with gene-pyramiding, they are still useful in breeding. Or, as technology continues to improve, gene knockouts and silencing of homologs may be employed to generate mutants in diverse species. If research continues to suggest crosstalk between ISR, SAR and insect defense signaling pathways, there may be great potential for additive defense effects by manipulating overlapping components. So, while limitations and cost of engineering broad-spectrum defenses warrant much attention, it is useful to look at such challenges as means for streamlining and improving upon current engineering strategies.Another promising strategy for enhancing resistance in plants is the use of RNA homology-dependent silencing to combat viral and bacterial disease . The nature of this silencing has been evaluated in a number of systems where similar phenomena are called by different names; RNAi in animals and quelling in fungi . One conserved step leading to RNA homology dependent silencing is the formation of a double stranded RNA intermediate. This dsRNA intermediate is recognized by an enzymatic complex which targets degradation of all corresponding homologous RNA transcripts . Several cases detailed below illustrate the possibilities for generating disease resistant plants by taking advantage of this inherent biological process.Viral resistance using RNA homology-dependent silencing has been successfully engineered into many plant systems. Single or multiple viral-derived transgenes can be expressed in plants leading to RNA homology-dependent silencing and subsequent viral resistance.

The use of this transgenic technology may be particularly effective in thwarting viral diseases where little or no genetic resistance has been identified. Resistance to rice yellow mottle virus is one example where traditional breeding cannot be used for improvement due to fertility barriers and genetic resistance being a poorly defined polygenic trait . The RYMV open reading frame 2 was highly expressed in transgenic rice. The resultant RYMV resistant lines carried very low or non-detectable amounts of the ORF2 RNA transcript. Conversely, transgenic lines that were susceptible had abundant amounts of the ORF2 transcript. Therefore the resistance phenotype was correlated with the loss of the viral transgene expression. This indicates that the mechanism of resistance was due to silencing of the ORF2 present as the transgene and in the RYMV RNA genome. The ORF2 sequence variation among different RYMV field isolates was found to be less than 10% at the nucleotide level suggesting that an RNA homology-dependent silencing approach may be effective in the field . Viral resistance utilizing endogenous silencing mechanisms is not restricted to using a single open reading frame from one virus. Two ORF fragments from different viruses can be fused into a chimeric expression cassette to confer resistance to both viruses. One clear example was generated from using tomato spotted wilt virus and turnip mosaic virus . The open reading frame for the N gene encoding the nucleocapsid from TSWV was fused to the coat protein of TuMV and the resulting chimeric construct was used to transform tobacco. As with the example using RYMV,resistance of the transgenic plants to both viruses corresponded with the loss of transcript accumulation from both viruses as detected by northern analysis. Transgenic plants susceptible to both viruses showed accumulation of the gene fragment transcript for both viruses. These two examples have been evaluated in greenhouse experiments; however, a well-described example of RNA homology-dependent silencing for viral resistance is presently being utilized successfully in the field.One clear commercial success of generating enhanced resistance by stable expression of a viral gene is against the papaya ring spot virus . Papaya is grown throughout the tropics and subtropics and no natural resistance has been described for PRSV. A PRSV control strategy for the Hawaiian islands was developed using RNA homology-dependent silencing by expressing a mutated open reading frame for the coat protein from PRSV . Resistant transgenic plants were generated and were found to be devoid of the CP RNA indicating the RNA homology-dependent silencing of the plant-derived transgene and PRSV gene . All PRSV strains present in Hawaii have been effectively controlled using silencing constructs derived from this mutant CP ORF. Sequence analysis demonstrated that these Hawaiian isolates had 97% or greater sequence homology to the mutant CP transgene. However, isolates of PRSV from outside of Hawaii can cause disease on the transgenic papaya lines. These geographically distinct isolates were found to have a lower sequence homology to the CP than the isolates from Hawaii. Thus, silencing of PRSV was contingent upon levels of sequence homology above 97% . Interestingly, PRSV and RYMV require different levels of homology between transgene and the endogenous gene to induce silencing. The silencing in RYMV was successful for all variations tested as compared with less than 3% divergence allowed for successful silencing in PRSV. Silencing is not only dependent upon the degree of homology but also the target sequence that is chosen. Much like the transgenic approach with R genes, each silencing construct must be carefully validated. Overall, RNA homology-dependant silencing has proven its utility in both the greenhouse and the field, and appears to be among the most versatile mechanisms currently available to engineer resistance to viruses.Crown-gall is a perennial problem in nurseries of fruit trees, nut trees and some bushy ornamental plants. Prevention of gall formation is a target for engineering resistance in these trees since breeding programs for resistance are not practical due to temporal considerations . When replanted, the trunks suffer cuts that are an entry point for the bacterium Agrobacterium tumefaciens, the causal agent of the disease, and infection becomes apparent with the formation of galls.

The fact that Sonora carries the day length sensitivity allele may seem surprising as it originates from Mexico. However, Sonora is thought to have been selected from a landrace that was brought over to the Americas from Europe with Columbus in 1492 and Shcherban et al. showed that 91% of spring wheat cultivars in Europe contain the photoperiod sensitive allele Ppd-D1b. A second consistent QTL for days to heading was identified on chromosome arm 5AL in the SF and CF populations. In SF the QTL covered a 4.4 cM region with a peak at 163 cM between markers 5A_10843 and 5A_24477 and explaining 20-21 % of the phenotypic variation. The QTL in the CF population covered a 10.4 cM region with its peak at 92 cM between the markers 5A_1737 and 5A_12135 explaining 18-28 % of the phenotypic variation. Although the markers are not identical they map within a couple of cM of one another in the consensus map of Wang et al. strongly suggesting that this is indeed the same QTL. The third QTL for days to heading was on the long arm of chromosome 5B in the SF and CF populations. In SF the QTL covers a region of 2.2 and 10.1 with peaks at 120 and 126 being that there was a slight shift between years from 5B_3483 and 5B_9459 in 2013 to 5B_80245 and 5B_3483 in 2014. This created a larger cM region and a 6 cM shift in the peak of the QTL for 2014. This QTL explains 17-20 % of the phenotypic variation seen in this population. For CF the QTL covers a 1.6 cM region with its peak around 106 cM between the markers 5B_80245 and 5B_51408 explaining 17 % of the phenotypic variation seen in this population.

These populations share the 5B_80245 marker providing validation of the QTL. Additional validation comes from Zanke et al. who located a gene on chromosome 5B related to the Hd6 gene family of rice with a major impact on heading time in wheat. They found that the marker Kukri_c10016_369 was the closest linked marker to the locus,growing tomatoes hydroponically and it maps to the same genetic position as 5B_3483 identified in our mapping experiments. This suggests that the QTL identified in two of our populations across multiple years is indeed this same Hd6 related locus. It is possible that the other QTL identified on 5A and 5D are homoeologous to the 5B QTL. This of course is only speculative and would require further inquiry. The fourth QTL was identified on the long arm of chromosome 5D in the SC and SF populations. For SC the QTL covers a 2.0 and 24.5 cM region with its peak between 78 and 75 cM respectively. A shift from 5D_17130 and 5D_502 in 2013 to 5D_4695 and 5D_17130 in 2014 cause the differences seen in QTL area and peak position, however, in both years the QTLs share marker 5D_17130. The QTL explains 45-49 % of the phenotypic variation seen in this population. In SF the QTL covers a region of 21.7 cM with a peak at 10 cM between the markers 5D_17310 and 5D_42321 and shares the 5D_17310 in common with the SC QTL. This QTL explains 29-41 % of the phenotypic variation seen in this population. Finally, the fifth QTL was located on the long arm of chromosome 5D and identified in the SC and CF populations. In the SC population it covers a 19.0 and 10.7 cM region with a peak around 150 and 156 cM, respectively. This QTL explains 40-52 % of the phenotypic variation found in the population. In 2013 the left and right markers were 5D_1682 and 5D_63558 while in 2014 the markers were 5D_63588 and 5D_5776 with marker 5D_63558 appearing in both years. The large region of this QTL is likely due to poor coverage of SNP markers on most of the D genome chromosomes. This QTL was also observed in the CF population where it covered a 7.6 cM region with a peak at 139 cM between markers 5D_63558 and 5D_5776 and explaining 22-25 % of the phenotypic variation in this population.

Both populations share markers 5D_63588 and 5D_5776 providing good validation for this QTL. When comparing days to heading in the greenhouse and the field it is apparent that the 18 hours of supplemental light given in the greenhouse greatly reduced the flowering time of the populations. This difference in treatment also enabled us to detect different flowering time loci. In the field only the day length sensitivity and insensitivity loci on 2D were detected, yet when grown under 18 hours of light all other QTLs were able to be identified. These other QTLs could potentially be Eps loci given that the photoperiod response was removed via the 18 hours of supplemental lighting provided. However, this speculation would require greater inquiry and further experiments to draw any solid conclusions.These include hybrid necrosis, hybrid chlorosis, and hybrid dwarfness with hybrid necrosis being encountered more frequently . Hermsen described hybrid necrosis as a premature and gradual death of foliage in certain hybrids. The trait is controlled by two dominant complementary genes Ne1 and Ne2 located on chromosome arms 5BL and 2BS respectively . In the three populations tested, hybrid necrosis was rated in the 2013 evaluations only and at which point all lines with unacceptable levels of necrosis were removed. Thus, QTL for hybrid necrosis were identified using the 2013 data for lines with acceptable levels of hybrid necrosis that were genotyped. Two QTLs were identified as being associated with hybrid necrosis in the CF population. The first is on chromosome arm 2BS where it covers a region of 0.8 cM with its peak at 82 cM between markers 2B_31805 and 2B_4614. It explains 22.51 % of the variation seen in the population.

The second QTL is on 5BL, covering a 1.6 cM region with a peak at 53 cM between the markers 5B_29636 and 5B_67642. It explains 31.16 % of the variation seen in the population. These two QTL may be the Ne1 and Ne2 genes but scoring would perhaps have to be repeated to verify the QTLs across years. It is likely that these QTLs were only seen in the CF population since both SF and SC had few lines expressing the trait included in genotyping, whereas CF had more lines expressing the trait that were included in genotyping.With persistent predictions of climate change and increased incidence of drought, crop root systems have gained serious attention. One of the challenges in this line of research is which root traits to focus on and in what environments these traits would be important; another one is to understand how root system traits are associated with one another and what trade-offs at the whole plant level are involved. Most root morphological traits appear to be regulated by a number of small-effect loci that interact with the environment. This becomes very apparent even at the earliest stages of experiments looking at root biomass and length. Natural plasticity induced by the environment creates large deviations that often obscure the genetic component of the observable phenotype. For these reasons de Dorlodot et al. suggested that processbased traits such as growth rate, branching frequency and tropism should be studied as opposed to “static traits” such as length, mass, and volume. Some studies have focused on incorporating traits from wild relatives or via new synthetic wheat . Others have looked at associations of root system traits and plant height and many have now begun to focus on seminal root traits. It has been suggested that, in the context of drought,ebb and flow bench roots targeting water acquisition deep in the soil profile may be especially important for smaller statured plants such as rice, wheat, and common bean . By measuring the amount of total water extracted from soil-filled root observation chambers and root growth pattern data Manschadi et al. estimated that each additional millimeter of water extracted during grain filling generated an additional 55kg ha-1 of grain yield.

Lynch proposed an ideotype for maize roots that included narrow seminal root angles with abundant lateral branching which would optimize water and nitrogen acquisition; this ideotype may also be relevant to other cereal root systems. Narrow seminal root angle generates a root system growing more downward into the soil profile, and presumably, reaching lower soil levels. In contrast, a wide angle of seminal roots appears to promote lateral root growth, a habit that may be beneficial in wetter conditions and under artificial irrigation. With frequent irrigation or rainfall, a root system distributed mainly in the upper soil layers would presumably provide quicker access to water and nutrient, without any cost to the plant for building deep-reaching roots. Oyanagi first began to investigate the inheritance of the geotropic response of seminal roots in wheat and concluded that the trait was simple, being controlled by a single locus, and his continued work contributed to the basis for our understanding of seminal root angle physiology in wheat . Those studies made observations on root distribution patterns and seminal root growth characteristics dependent upon the target environment for which specific cultivars were selected. Typically, cultivars adapted to regions with limited rainfall had narrower seminal root angle and deeper root systems; wheats adapted to environments with higher rainfall and/or irrigation tend to have wide seminal root angles which, presumably, facilitate water and nutrient acquisition from a wider sub-surface area. Following these ideas, Manschadi et al. investigated seminal root angle and discovered a large amount of genetic diversity within the panel of screened cultivars. Their cluster analysis has shown that groups of wheat with similar seminal root characteristics reflected the genetic background and environmental adaptation. Those observations are supported by other research linking root distribution to improved agronomic performance and canopy temperature depression under heat and drought stress . Seminal root traits are relatively simple to score and do not require complex experimental systems. This makes them an aspect of choice in root system studies. Drawing ideas from maize studies, Oyanagi suggested that gravitropic responses of roots would be predictive of wheat root distribution in the soil. That idea was supported by Manschadi et al. who found that root system architecture is closely linked to the angle of seminal root growth at the seedling stage. Those findings led to a suggestion that selection for the growth angle and the number of seminal roots may identify genotypes better suited for drought conditions. Measuring root traits of mature plants in the field is a daunting task; for entire mapping populations it is practically impossible. Perhaps for this reason, seminal root traits of seedlings are the favorite research target as they can be measured in several simple experimental set-ups. For all these reasons, studies of seminal root traits appear justified, by providing observations of simple parameters of root architecture, especially when dealing with hundreds of genotypes at a time. At some point all observations of such proxy indicators would have to be verified by screening in the field with a limited number of genotypes. The results presented here add to earlier foundational work, and begin to unravel the genetics behind some aspects of root system architecture. The emerging picture is far more complicated than originally suggested by Oyanagi . While seminal root angle shows high heritability, it clearly is a quantitative trait with a complicated pattern of inheritance. Seminal root angles and numbers were phenotyped in three doubled haploid populations of bread wheat. These populations were created by pair-wise crossing of three landrace cultivars with contrasting root phenotypes. Cv. Sonora has shallow seminal roots growing at wide angles, and cvs. Foisy and Chiddam Blanc de Mars have deep seminal roots with narrow angles. Crosses were made in a triangular fashion so that each of the three parents is present in two of the populations. This arrangement provides a built in system for verification of QTL identified across populations and genetic backgrounds. Detailed information about genotyping, linkage mapping and general descriptions of each population can be found in the previous chapter of this dissertation.

Phosphonates can also serve as a source of phosphorus or carbon for a variety of microorganisms and several pathways for phosphonate degradation have been characterized . For example, some bacteria can use methylphosphonate as a P source in a process that releases methane and inorganic phosphate . This process is catalyzed by the C-P lyase enzyme and involves a phosphate radical intermediate . Under mildly reducing conditions phosphate radicals can rearrange to form phosphite, making it a possible byproduct of methylphosphonate degradation in anaerobic environments . Moreover, phosphonates with carbonyl or hydroxyl groups at the α-carbon, such as phosphonoformic acid, tend to form phosphite rather than phosphate as the product of C-P cleavage even under oxidizing conditions . Given that C-P lyase enzymes are involved in the degradation of a variety of phosphonates, it is possible that these reactions are a significant source of environmental phosphite. Biological phosphate reduction has also been posited as a possible source of environmental phosphite. Devai and colleagues detected phosphine gas production in wastewater and marsh soils and showed that phosphine production was stimulated by the addition of inorganic phosphate and organic matter, leading them to conclude that phosphate was being reduced to phosphine by microorganisms present in their samples . Some of this phosphine could subsequently be oxidized to phosphite in the presence of O2or UV radiation . However,hydroponic grow kit the conclusion by Devai et al. that the phosphine they observed was derived from biological phosphate reduction has since been questioned by several researchers .

Roels and coworkers have noted that biological phosphate reduction is problematic from a thermodynamic standpoint, since there is no known biological electron donor with a low enough redox potential to make the reaction exergonic . Glindemann and coworkers have shown that phosphine can be produced during the corrosion of iron, even under sterile conditions . This is due to the fact that iron minerals often contain phosphorus impurities that can be abiotically reduced to iron phosphides during the industrial smelting process and these phosphides can then be released as phosphine gas during corrosion . Subsequent studies have likewise concluded that phosphine is released due to iron corrosion and that the higher rates of phosphine production observed in the presence of microorganisms is likely due to the microbial production of organic acids and hydrogen sulfide, which accelerate the corrosion process . Although evidence of biological phosphate reduction remains inconclusive, several theoretical mechanisms by which this process could occur have been proposed. Pasek and colleagues have suggested that in addition to being produced during phosphonate degradation, phosphite could also be formed as a byproduct of phosphonate biosynthesis in reducing environments . They determined that the reductive cleavage of phosphoenolpyruvate by H2 to form phosphite and pyruvate is thermodynamically feasible under standard cellular conditions . Given that phosphoenolpyruvate is a key intermediate in the production of phosphonates from inorganic phosphate, such a mechanism would be a way of indirectly converting phosphate to phosphite. A more direct mechanism of phosphate reduction has been proposed by Roels and colleagues, who note that the reduced molybdoferredoxin cofactor of the nitrogenase complex has a redox potential of -1.0 V, which is low enough to reduce phosphate to phosphite .

However, they question the usefulness of such a reaction since energy from ATP hydrolysis must be expended in order to achieve such a low reduction potential and the organism would gain nothing from the production of phosphite. Nevertheless, it is possible that phosphite may be formed as an unwanted product of nitrogenase function in the presence of phosphate. This sort of inadvertent phosphate reduction might also occur in photosynthetic organisms, since the redox potentials of excited reaction center chlorophyll molecules range from -0.8 V to -1.26 V . Environments dominated by anoxygenic phototrophs may therefore be potential hot spots of biological phosphite production since the absence of strong oxidants in these systems would favor the accumulation of reduced phosphorus species. produced would have to be diverted for use in anabolic reactions.FiPS-3, on the other hand, uses PtdC as its phosphite transporter instead of PtxABC. If PtdC does, in fact, function as a phosphite/phosphate antiporter as has been proposed, then there would be no energy cost associated with phosphite uptake in FiPS-3 . However, when both PtxD and PtdC were expressed in SaxT, it still did not gain the ability to grow by DPO, which indicates that an additional mechanism of energy conservation, possibly mediated by the ptdFGHI genes, is required in this organism. In contrast to P. stutzeri, FiPS-3 and SaxT growing by sulfate reduction would gain substantially less energy from NADH oxidation. During sulfate reduction 2 ATP must be initially expended in order to activate and reduce sulfate to sulfite, which can then be further reduced to sulfide in an exergonic reaction . Sulfate reducing bacteria growing on H2 typically generate 3 ATP from the sulfite reduction step for a net overall production of 1 mol ATP per mol sulfate reduced, which corresponds to the expected yield based on equation 4 .

However, if sulfite reduction were instead coupled to NADH oxidation according to equation 5 , the expected yield would only be 2 mol ATP per mol sulfite reduced, which would result in no net ATP production from the overall reduction of sulfate . In order to grow by DPO, therefore, FiPS-3 and SaxT would not only need to save energy on phosphite uptake, but also conserve more of the free energy available from the oxidation of phosphite. The NAD+ /NADH couple has a redox potential of -320 mV under standard physiological conditions , which means that the reduction of NAD+ coupled to phosphite oxidation releases 63.7 kJ.mol-1 phosphite. This additional energy is presumably lost in traditional APO-capable organisms, but there is evidence that it is conserved in FiPS-3. Schink and coworkers observed substantially higher cell yields when FiPS-3 was grown on phosphite and sulfate versus formate and sulfate . Since phosphite and formate both donate 2 electrons and the redox potential of the CO2/formate couple is actually higher than that of NAD+ /NADH , the higher yields seen on phosphite are not consistent with NADH oxidation being the sole means of ATP production during DPO. Furthermore,vertical farming racks the growth yield of FiPS-3 on phosphite and CO2 via the Wood-Ljungdahl pathway was about 10 times higher than the yields typically observed for other Wood-Ljungdahl acetogens growing on H2 and CO2, such as Acetobacterium woodiiand Acetogenium kivui . These results suggest that FiPS-3 can in fact take advantage of the extremely electronegative redox potential of phosphite, although it is unclear how this is accomplished since there are no known biological redox carriers that can accept electrons at such a low potential . Schink and coworkers have proposed that ATP is generated from phosphite oxidation by means of substrate level phosphorylation in addition to the reduction of NAD+ , thus yielding both energy and reducing equivalents for each molecule of substrate utilized . Such a reaction would be thermodynamically feasible according to equation 6 . Therefore, the function of the ptdFGHI genes may be to facilitate substrate level phosphorylation during phosphite oxidation . Relyea and van der Donk have suggested that one of the possible mechanisms of phosphite oxidation by PtxD may involve the creation of a phosphorylated enzyme intermediate that is subsequently hydrolyzed to release phosphate . PtdFGHI might interact with PtxD in order to facilitate the transfer of this phosphoryl group to ADP, either directly or by means of additional phosphorylated intermediates.

This is a promising avenue for future inquiry but more work is currently necessary in order to determine whether phosphite acts as a phosphoryl donor for ATP synthesis during DPO and what role, if any, the ptdFGHI genes play in this process. Over the last 20 years, the study of reduced phosphorus compounds and their role in nature has grown from a series of curious observations and intriguing theories into an exciting new frontier in biogeochemistry. In particular, recent discoveries regarding the geochemistry and biology of phosphite have highlighted the potential significance of this compound both as a facilitator for the emergence of life on ancient Earth and as a modern driver of microbial processes that continue to shape the global biosphere. Phosphite has been detected in several environments at concentrations that suggest the current existence of a phosphorus redox cycle occurring at short geological timescales. Several anthropogenic sources of phosphite have been identified, and there is evidence that phosphite may also be produced by natural processes such as biological phosphonate metabolism and geothermal phosphate reduction. The presence of the genes responsible for assimilatory phosphite oxidation in hundreds of microbial isolates from a variety of environments indicates that this process is widespread and may have a substantial impact on the global P cycle. Furthermore, the discovery of dissimilatory phosphite oxidation and its ability to sustain carbon fixation while providing an energetic benefit raises the possibility of phosphite as a key, though hitherto unrecognized, driver of primary productivity in the environment. Several milligrams of mineral precipitates were sampled from FiPS-3 cultures grown on phosphite with either calcium or magnesium in the media and mineral samples were ground into a powder. For SEM, a sample of the powdered mineral was suspended in several milliliters of distilled water to create a mineral slurry.A drop of the mineral slurry was fixed with 2% glutaraldehyde in 0.1 M sodium cacodylate buffer, added to the silicon wafers, and allowed to settle for 1 h. Samples were then dehydrated for 10 min in 35%, 50%, 70%, 80%, 95%, and 100% ethanol, followed by critical point drying. Dehydrated samples were mounted onto stubs, sputter coated with palladium/gold, and visualized using a Hitachi S-5000 scanning electron microscope at 20 kV. For XRD, a sample of the powdered mineral was suspended in a few drops of amyl acetate to create a mineral slurry. The mineral slurry was then analyzed with a PANalytical X’Pert Pro diffractometer equipped with a Co x-ray tube and an X’Celerator detector. In accordance with previous observations, DPO-dependent growth of FiPS-3 was accompanied by the appearance of mineral precipitates in the medium several days after the onset of phosphite oxidation . The precipitates appeared to be crystalline and varied in size from several millimeters to several centimeters in length. Typically, some of the crystals would adhere to the bottom and sides of the glass culture tubes, although most would remain suspended in the medium. No precipitates were observed in cultures grown with fumarate as the electron donor instead of phosphite . Subsequent tests showed that DPO-dependent biomineralization could be used to consolidate a fine-grained calcium carbonate matrix at standard temperature and pressure and circumneutral pH. When FiPS-3 was grown in the presence of phosphite, all of the calcium carbonate present in the media was consolidated into a hardened mineral phase that adhered to the bottom of the glass culture bottles, whereas in FiPS-3 cultures grown on fumarate or in sterile phosphite-containing media the calcium carbonate particles remained suspended in the liquid phase . SEM imaging of precipitates from FiPS-3 cultures amended with either calcium or magnesium showed different mineral morphologies depending on which cation was present in the media . Analysis of the precipitates using XRD confirmed that they were crystalline phosphate minerals and that their chemical compositions varied based on the cation present. Hydroxyapatite 26) was produced in the presence of calcium, whereas struvite was produced in the presence of magnesium. The SEM images also appeared to show that some of the cells involved in the biomineralization process became embedded in the mineral phase . Genomic analysis suggested that FiPS-3 was incapable of synthesizing phenylalanine and histidine, and addition of these amino acids to the growth media did indeed result in a drastic reduction in cell doubling time and increase in maximum OD. However, FiPS-3 was still able to grow, albeit poorly, in the absence of phenylalanine and histidine, indicating that it is still able to make these amino acids even though it appears to be missing genes in both biosynthetic pathways.